Docstringed MDANSE.Core.Preferences module

Reintroduced and refactored several analysis

MDANSE/App/GUI/ControllerPanel.py

@@ -5,7 +5,7 @@ import wx.aui as wxaui
 import wx.py as wxpy
 
 from MDANSE.App.GUI.JobControllerPanel import JobControllerPanel
-from MDANSE.App.GUI.Icons import ICONS, scaled_bitmap
+from MDANSE.App.GUI.Icons import ICONS
 
 class ControllerPanel(wx.Panel):
 
@@ -33,9 +33,9 @@ class ControllerPanel(wx.Panel):
         #wxpython 2.9 compatibility
         if wx.VERSION[:2] > (2,8):
             il = wx.ImageList(16, 16)
-            il.Add(scaled_bitmap(ICONS["log"], 16,16))
-            il.Add(scaled_bitmap(ICONS["shell"], 16,16))
-            il.Add(scaled_bitmap(ICONS["hourglass"], 16,16))
+            il.Add(ICONS["log",16,16])
+            il.Add(ICONS["shell",16,16])
+            il.Add(ICONS["hourglass",16,16])
             self._notebook.AssignImageList(il)
     
             self._notebook.AddPage(self._pages["logger"], 'Logger')                   
@@ -47,9 +47,9 @@ class ControllerPanel(wx.Panel):
             self._notebook.SetPageImage(2, 2)
 
         else:
-            self._notebook.AddPage(self._pages["logger"], 'Logger', bitmap=scaled_bitmap(ICONS["log"], 16,16))                   
-            self._notebook.AddPage(self._pages["console"], 'Console', bitmap=scaled_bitmap(ICONS["shell"], 16,16))
-            self._notebook.AddPage(self._pages["jobs"], 'Jobs', bitmap=scaled_bitmap(ICONS["hourglass"], 16,16))
+            self._notebook.AddPage(self._pages["logger"], 'Logger', bitmap=ICONS["log",16,16])                   
+            self._notebook.AddPage(self._pages["console"], 'Console', bitmap=ICONS["shell",16,16])
+            self._notebook.AddPage(self._pages["jobs"], 'Jobs', bitmap=ICONS["hourglass",16,16])
     
     def build_layout(self):
         

MDANSE/App/GUI/JobControllerPanel.py

@@ -48,7 +48,7 @@ from MDANSE.Framework.Jobs.JobStatus import JobState
 from MDANSE.Externals.pubsub import pub
 from MDANSE.Logging.Logger import LOGGER
 
-from MDANSE.App.GUI.Icons import ICONS, scaled_bitmap
+from MDANSE.App.GUI.Icons import ICONS
 from MDANSE.App.GUI.Events.JobControllerEvent import EVT_JOB_CONTROLLER, JobControllerEvent
         
 class JobController(threading.Thread):
@@ -196,7 +196,7 @@ class JobControllerPanel(wx.ScrolledWindow):
         state = wx.TextCtrl(self, wx.ID_ANY, style=wx.TE_READONLY|wx.ALIGN_CENTER_HORIZONTAL)
         progress = wx.Gauge(self, wx.ID_ANY,range=100)
         eta = wx.TextCtrl(self, wx.ID_ANY, style=wx.TE_READONLY|wx.ALIGN_CENTER_HORIZONTAL)
-        kill = wx.BitmapButton(self, wx.ID_ANY, scaled_bitmap(ICONS["stop"], 24, 24))
+        kill = wx.BitmapButton(self, wx.ID_ANY, ICONS["stop",24,24])
 
         self._gbSizer.Add(name    ,pos=(r,0),flag=wx.EXPAND|wx.ALIGN_CENTER_HORIZONTAL)
         self._gbSizer.Add(pid     ,pos=(r,1),flag=wx.EXPAND|wx.ALIGN_CENTER_HORIZONTAL)

MDANSE/App/GUI/MainFrame.py

@@ -9,7 +9,7 @@ from MDANSE import LOGGER, REGISTRY
 from MDANSE.App.GUI import DATA_CONTROLLER
 from MDANSE.App.GUI.ControllerPanel import ControllerPanel
 from MDANSE.App.GUI.DataTreePanel import DataTreePanel
-from MDANSE.App.GUI.Icons import ICONS, scaled_bitmap
+from MDANSE.App.GUI.Icons import ICONS
 from MDANSE.App.GUI.PluginsTreePanel import PluginsTreePanel
 from MDANSE.App.GUI.WorkingPanel import WorkingPanel
 
@@ -34,7 +34,7 @@ class MainFrame(wx.Frame):
         self.build_toolbar()
 
         icon = wx.EmptyIcon()
-        icon.CopyFromBitmap(scaled_bitmap(ICONS["nmoldyn"], 32, 32))
+        icon.CopyFromBitmap(ICONS["nmoldyn",32,32])
         self.SetIcon(icon) 
         
         # The main aui manager.
@@ -98,18 +98,18 @@ class MainFrame(wx.Frame):
         
         self._toolbar = self.CreateToolBar()
                 
-        loadDataButton = self._toolbar.AddSimpleTool(wx.ID_ANY, scaled_bitmap(ICONS["load"], 32, 32), 'Load a trajectory')
-        emptyDataButton = self._toolbar.AddSimpleTool(wx.ID_ANY, scaled_bitmap(ICONS["empty_data"], 32, 32), 'Open an empty data (converters ...)')
-        databaseButton = self._toolbar.AddSimpleTool(wx.ID_ANY, scaled_bitmap(ICONS["periodic_table"], 32, 32), 'Edit the nMolDyn elements database')
-        plotButton = self._toolbar.AddSimpleTool(wx.ID_ANY,scaled_bitmap(ICONS["plot"], 32, 32), 'Open nMolDyn plotter')
-        userButton = self._toolbar.AddSimpleTool(wx.ID_ANY,scaled_bitmap(ICONS["user"], 32, 32), 'Edit the user definitions')
-        preferencesButton = self._toolbar.AddSimpleTool(wx.ID_ANY, scaled_bitmap(ICONS["preferences"], 32, 32), 'Edit the preferences')
-        logfileButton = self._toolbar.AddSimpleTool(wx.ID_ANY, scaled_bitmap(ICONS["logfile"], 32, 32), 'Display nMOLDYN log file')
-        helpButton = self._toolbar.AddSimpleTool(wx.ID_ANY, scaled_bitmap(ICONS["help"], 32, 32), 'Help')
-        websiteButton = self._toolbar.AddSimpleTool(wx.ID_ANY, scaled_bitmap(ICONS["web"], 32, 32), 'Open nMoldyn website')
-        aboutButton = self._toolbar.AddSimpleTool(wx.ID_ANY, scaled_bitmap(ICONS["about"], 32, 32), 'About nMolDyn')
-        bugButton = self._toolbar.AddSimpleTool(wx.ID_ANY, scaled_bitmap(ICONS["bug"], 32, 32), 'Bug report')
-        quitButton = self._toolbar.AddSimpleTool(wx.ID_ANY, scaled_bitmap(ICONS["quit"], 32, 32), 'Quit nMoldyn')
+        loadDataButton = self._toolbar.AddSimpleTool(wx.ID_ANY, ICONS["load",32,32], 'Load a trajectory')
+        emptyDataButton = self._toolbar.AddSimpleTool(wx.ID_ANY, ICONS["empty_data",32,32], 'Open an empty data (converters ...)')
+        databaseButton = self._toolbar.AddSimpleTool(wx.ID_ANY, ICONS["periodic_table",32,32], 'Edit the MDANSE elements database')
+        plotButton = self._toolbar.AddSimpleTool(wx.ID_ANY,ICONS["plot",32,32], 'Open MDANSE plotter')
+        userButton = self._toolbar.AddSimpleTool(wx.ID_ANY,ICONS["user",32,32], 'Edit the user definitions')
+        preferencesButton = self._toolbar.AddSimpleTool(wx.ID_ANY, ICONS["preferences",32,32], 'Edit the preferences')
+        logfileButton = self._toolbar.AddSimpleTool(wx.ID_ANY, ICONS["logfile",32,32], 'Display nMOLDYN log file')
+        helpButton = self._toolbar.AddSimpleTool(wx.ID_ANY, ICONS["help",32,32], 'Help')
+        websiteButton = self._toolbar.AddSimpleTool(wx.ID_ANY, ICONS["web",32,32], 'Open MDANSE website')
+        aboutButton = self._toolbar.AddSimpleTool(wx.ID_ANY, ICONS["about",32,32], 'About MDANSE')
+        bugButton = self._toolbar.AddSimpleTool(wx.ID_ANY, ICONS["bug",32,32], 'Bug report')
+        quitButton = self._toolbar.AddSimpleTool(wx.ID_ANY, ICONS["quit",32,32], 'Quit MDANSE')
         
         self._toolbar.Realize()
         

MDANSE/App/GUI/__init__.py

@@ -7,27 +7,9 @@ if platform.dist()[0].lower() == "ubuntu":
         
 from MDANSE.App.GUI.DataController import DATA_CONTROLLER
 
-import glob
-import sys
+from MDANSE import REGISTRY
 
 directories = sorted([x[0] for x in os.walk(os.path.dirname(__file__))][1:])
 
 for d in directories:
-         
-    for module in glob.glob(os.path.join(d,'*.py')):
-                         
-        moduleDir, moduleFile = os.path.split(module)
- 
-        if moduleFile == '__init__.py':
-            continue
- 
-        moduleName, moduleExt = os.path.splitext(moduleFile)
-
-        if moduleDir not in sys.path:        
-            sys.path.append(moduleDir)
-                  
-        # Any error that may occur here has to be caught. In such case the module is skipped.    
-        try:
-            __import__(moduleName, locals(), globals())
-        except:
-            continue
+    REGISTRY.update_registry(d)
\ No newline at end of file

MDANSE/Core/ClassRegistry.py

@@ -31,8 +31,10 @@ Created on Mar 30, 2015
 '''
 
 import abc
+import glob
 import inspect
 import os
+import sys
 
 class _Meta(type):
     '''
@@ -98,13 +100,46 @@ class ClassRegistry(abc.ABCMeta):
                 if issubclass(self, interface):
                     ClassRegistry._registry[interface.type][typ] = self
                     break
+          
+    @classmethod      
+    def update_registry(cls,packageDir):
+        '''
+        Update the classes registry by importing all the modules contained in a given package.
+        
+        Only the classes that are metaclassed by ClassRegistry will be registered.
+        
+        :param cls: the ClassRegistry instance
+        :type: ClassRegistry
+        :param packageDir: the package for which all modules should be imported
+        :type packageDir: str
+        '''
                 
+        for module in glob.glob(os.path.join(packageDir,'*.py')):
+                             
+            moduleDir, moduleFile = os.path.split(module)
+     
+            if moduleFile == '__init__.py':
+                continue
+     
+            moduleName, moduleExt = os.path.splitext(moduleFile)
+            
+            print moduleName
+    
+            if moduleDir not in sys.path:        
+                sys.path.append(moduleDir)
+                      
+            # Any error that may occur here has to be caught. In such case the module is skipped.    
+            try:
+                __import__(moduleName, locals(), globals())
+            except:
+                continue
+    
     @classmethod
     def info(cls, interface):
         '''
         Returns informations about the subclasses of a given base class  stored in the registry.
         
-        :param cls: the ClassRegsitry instance
+        :param cls: the ClassRegistry instance
         :type cls: ClassRegistry
         :param interface: the name of base class of whom information about its subclasses is requested
         :type interface: str

MDANSE/Core/Preferences.py

+#MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
+#------------------------------------------------------------------------------------------
+#Copyright (C)
+#2015- Eric C. Pellegrini Institut Laue-Langevin
+#BP 156
+#6, rue Jules Horowitz
+#38042 Grenoble Cedex 9
+#France
+#pellegrini[at]ill.fr
+#goret[at]ill.fr
+#aoun[at]ill.fr
+#
+#This library is free software; you can redistribute it and/or
+#modify it under the terms of the GNU Lesser General Public
+#License as published by the Free Software Foundation; either
+#version 2.1 of the License, or (at your option) any later version.
+#
+#This library is distributed in the hope that it will be useful,
+#but WITHOUT ANY WARRANTY; without even the implied warranty of
+#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+#Lesser General Public License for more details.
+#
+#You should have received a copy of the GNU Lesser General Public
+#License along with this library; if not, write to the Free Software
+#Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+
+''' 
+Created on Mar 30, 2015
+
+@author: pellegrini
+'''
+
+import abc
+import collections
+import ConfigParser
+import os
+
+from MDANSE.Core.Platform import PLATFORM, PlatformError
+from MDANSE.Core.Error import Error
+from MDANSE.Core.Singleton import Singleton
+
+class PreferencesError(Error):
+    '''
+    This class handles the errors that occurs in Preferences.
+    '''
+    
+    pass
+
+class PreferencesItem(object):
+    '''
+    This is the base class for defining a preferences item.
+    
+    A preferences item implements is a light object used to check preferences before setting them
+    but also classify preferences according to their section for a further use in MDANSE GUI.
+    '''
+    
+    __metaclass__ = abc.ABCMeta
+
+    def __init__(self, name, section, default, *args, **kwargs):
+        '''
+        Constructor a new prferences item.
+        
+        :param name: the name of the preference item
+        :type name: str 
+        :param section: the section of the preferences item
+        :type section: str
+        :param default: the default value for the preferences item
+        :type default: str
+        '''
+        
+        self._name = name
+        
+        self._section = section
+        
+        self._default = default
+        
+        self._value = self._default
+                
+    @property
+    def default(self):
+        '''
+        Returns the default value of the preferences item.
+        
+        :return: the default value of the preferences item
+        :rtype: str
+        '''
+        
+        return self._default
+    
+    def get_default(self):
+        '''
+        Returns the default value of the preferences item.
+        
+        :return: the default value of the preferences item
+        :rtype: str
+        '''
+        
+        return self._default
+        
+    @property
+    def name(self):
+        '''
+        Returns the name of the preferences item.
+        
+        :return: the name of the preferences item
+        :rtype: str
+        '''
+
+        return self._name
+
+    def get_name(self):
+        '''
+        Returns the name of the preferences item.
+        
+        :return: the name of the preferences item
+        :rtype: str
+        '''
+
+        return self._name
+        
+    @property
+    def section(self):
+        '''
+        Returns the section of the preferences item.
+        
+        :return: the section of the preferences item
+        :rtype: str
+        '''
+
+        return self._section
+    
+    def get_section(self):
+        '''
+        Returns the section of the preferences item.
+        
+        :return: the section of the preferences item
+        :rtype: str
+        '''
+        
+        return self._section
+    
+    def reset(self):
+        '''
+        Reset the preferences item to its default value
+        '''
+        
+        self._value = self._default
+        
+    @property
+    def value(self):
+        '''
+        Returns the value of the preferences item.
+        
+        :return: the value of the preferences item
+        :rtype: str
+        '''
+
+        return self._value
+
+    def get_value(self):
+        '''
+        Returns the value of the preferences item.
+        
+        :return: the value of the preferences item
+        :rtype: str
+        '''
+
+        return self._value
+
+    @abc.abstractmethod
+    def set_value(self,value):
+        '''
+        Set the value of the preferences item.
+        
+        :param value: the value of the preferences item
+        :type value: str
+        '''
+        
+        pass
+
+class InputDirectory(PreferencesItem):
+    '''
+    This class implements a preferences item that handles an input directory.
+    
+    When set to a given input directory, if this one does not exists, it will be be created.
+    '''
+    
+    type = "input_directory"
+
+
+    def set_value(self, value):
+        '''
+        Set the value of the input directory preferences item.
+        
+        :param value: the input directory
+        :type value: str
+        '''
+        
+        value = PLATFORM.get_path(value)
+        
+        try:
+            PLATFORM.create_directory(value)
+        except PlatformError:
+            raise PreferencesError('Error when setting input directory %r' % value)
+        
+        self._value = value
+                
+class Preferences(collections.OrderedDict):
+    '''
+    This class implements the MDANSE preferences.
+    
+    Preferences are defined using the ConfigParser python module that allows to read and write 
+    preferences stored in a formatted INI file (RFC822).
+    '''
+    
+    __metaclass__ = Singleton
+    
+    def __init__(self):
+        '''
+        Constructs the preferences
+        '''
+        
+        self["working_directory"] = InputDirectory("working_directory", "paths", PLATFORM.home_directory())
+        self["macros_directory"] = InputDirectory("macros_directory", "paths", os.path.join(PLATFORM.home_directory(), "mdanse_macros"))
+                
+        self._parser = ConfigParser.ConfigParser()
+
+        for s in self._items.values():
+            try:
+                self._parser.add_section(s.section)
+            except ConfigParser.DuplicateSectionError:
+                pass
+                                                                    
+        # Overwrite the default preferences with the user defined loaded ones.
+        try:
+            self.load()
+        except PreferencesError:
+            pass
+        
+    @property
+    def parser(self):
+        '''
+        Returns the configuration parser object used to serialize the preferences.
+        
+        :return: the configuration parser bound to the preferences
+        :rtype: ConfigParser.ConfigParser
+        '''
+        return self._parser
+    
+    def __getitem__(self, item):
+        '''
+        Get the value of a selected preferences item.
+        
+        :param item: the preferences item
+        :type item: str
+
+        :return: the values of the preferences item.
+        :rtype: str
+        '''
+        
+        try:
+            value = self[item].value
+        except KeyError:
+            raise PreferencesError("The preferences item %r is not valid" % item)
+        else:
+            return value
+                
+    def __setitem__(self, item, value):
+        '''
+        Set the value of a preferences item.
+        
+        :param item: the preferences item
+        :type item: str
+        
+        :param value: the value to set for the preferences item.
+        :type value: any
+        '''
+        
+        if not self._items.has_key(item):
+            return
+
+        try:
+            self._items[item].value = value
+
+        except KeyError:
+            raise PreferencesError("The preferences item %r is not valid" % item)
+        
+    def load(self):
+        '''
+        Load the preferences from a preferences file.
+        '''
+                    
+        path = PLATFORM.preferences_file()
+
+        if not isinstance(path,basestring):
+            raise PreferencesError("Invalid type for preferences filename: %s" % path)
+        
+        if not os.path.exists(path):
+            raise PreferencesError("The preferences files %s does not exists. nMolDyn will use the default preferences." % path)
+                
+        try:
+            # Read the preferences and overwrites the nmoldyn default preferences.
+            self._parser.read(path)
+        except ConfigParser.ParsingError as e:
+            raise PreferencesError(e)
+        
+        for s in self._parser.sections():
+            for k, v in self._parser.items(s):
+                self[k] = v 
+                         
+    def save(self):
+        '''
+        Save the preferences to a file.        
+        '''
+        
+        path = PLATFORM.preferences_file()
+            
+        try:
+            f = open(path, "w")
+        except (IOError,TypeError) as e:
+            raise PreferencesError(e)
+
+        for v in self._items.values():
+            self._parser.set(v.section,v.name,v.value)
+                
+        # Write the preferences.
+        self._parser.write(f)
+        
+        # Closes the preferences file.
+        f.close()
+        
+PREFERENCES = Preferences()
\ No newline at end of file

MDANSE/Framework/Jobs/AngularCorrelation.py

+#MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
+#------------------------------------------------------------------------------------------
+#Copyright (C)
+#2015- Eric C. Pellegrini Institut Laue-Langevin
+#BP 156
+#6, rue Jules Horowitz
+#38042 Grenoble Cedex 9
+#France
+#pellegrini[at]ill.fr
+#goret[at]ill.fr
+#aoun[at]ill.fr
+#
+#This library is free software; you can redistribute it and/or
+#modify it under the terms of the GNU Lesser General Public
+#License as published by the Free Software Foundation; either
+#version 2.1 of the License, or (at your option) any later version.
+#
+#This library is distributed in the hope that it will be useful,
+#but WITHOUT ANY WARRANTY; without even the implied warranty of
+#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+#Lesser General Public License for more details.
+#
+#You should have received a copy of the GNU Lesser General Public
+#License along with this library; if not, write to the Free Software
+#Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+
+''' 
+Created on Apr 10, 2015
+